Obviously, I would recommend newbler from 454. However, there is also a program from the Broad specifically designed for your taks:
Quote:
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AV454 (AssembleViral454) is an assembler, based on the ARACHNE package, designed for small and non-repetitive genomes sequenced at high depth. It was specifically designed to assemble read data generated from a mixed population of viral genomes.
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Found
here.